Phosphate starvation signaling increases mitochondrial membrane potential through respiration-independent mechanisms

Mitochondrial membrane potential directly powers many critical functions of mitochondria, including ATP production, mitochondrial protein import, and metabolite transport. Its loss is a cardinal feature of aging and mitochondrial diseases, and cells closely monitor membrane potential as an indicator of mitochondrial health. Given its central importance, it is logical that cells would modulate mitochondrial membrane potential in response to demand and environmental cues, but there has been little exploration of this question. We report that loss of the Sit4 protein phosphatase in yeast increases mitochondrial membrane potential, both through inducing the electron transport chain and the phosphate starvation response. Indeed, a similarly elevated mitochondrial membrane potential is also elicited simply by phosphate starvation or by abrogation of the Pho85-dependent phosphate sensing pathway. This enhanced membrane potential is primarily driven by an unexpected activity of the ADP/ATP carrier. We also demonstrate that this connection between phosphate limitation and enhancement of the mitochondrial membrane potential is also observed in primary and immortalized mammalian cells as well as in Drosophila. These data suggest that mitochondrial membrane potential is subject to environmental stimuli and intracellular signaling regulation and raise the possibility for therapeutic enhancement of mitochondrial functions even with defective mitochondria.

[1]  A. Wojtovich,et al.  Optogenetic rejuvenation of mitochondrial membrane potential extends C. elegans lifespan , 2022, bioRxiv.

[2]  Matthew R. Clutter,et al.  Genes Involved in Maintaining Mitochondrial Membrane Potential Upon Electron Transport Chain Disruption , 2022, Frontiers in Cell and Developmental Biology.

[3]  F. Broeskamp,et al.  Phosphate Restriction Promotes Longevity via Activation of Autophagy and the Multivesicular Body Pathway , 2021, Cells.

[4]  Brandon J. Berry,et al.  Decreased Mitochondrial Membrane Potential Activates the Mitochondrial Unfolded Protein Response , 2021, microPublication biology.

[5]  She Chen,et al.  OXPHOS deficiency activates global adaptation pathways to maintain mitochondrial membrane potential , 2021, EMBO reports.

[6]  K. Parnell,et al.  The pyruvate-lactate axis modulates cardiac hypertrophy and heart failure. , 2020, Cell metabolism.

[7]  T. Enver,et al.  Mitochondrial Potentiation Ameliorates Age-Related Heterogeneity in Hematopoietic Stem Cell Function. , 2020, Cell stem cell.

[8]  Sara M. Nowinski,et al.  Mitochondrial fatty acid synthesis coordinates oxidative metabolism in mammalian mitochondria , 2020, eLife.

[9]  T. Cameron Waller,et al.  Network-aware reaction pattern recognition reveals regulatory signatures of mitochondrial dysfunction , 2021 .

[10]  Ramin Rad,et al.  Improved Monoisotopic Mass Estimation for Deeper Proteome Coverage , 2020, bioRxiv.

[11]  Devin K. Schweppe,et al.  TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples , 2020, Nature Methods.

[12]  A. Trewin,et al.  Optogenetic control of mitochondrial protonmotive force to impact cellular stress resistance , 2020, EMBO reports.

[13]  Mi-Young Jeong,et al.  Cysteine Toxicity Drives Age-Related Mitochondrial Decline by Altering Iron Homeostasis , 2020, Cell.

[14]  Aaron R. Quinlan,et al.  XPRESSyourself: Enhancing, Standardizing, and Automating Ribosome Profiling Computational Analyses Yields Improved Insight into Data , 2019, bioRxiv.

[15]  K. Kuhn,et al.  TMTpro: Design, synthesis and initial evaluation of a Proline-based isobaric 16-plex Tandem Mass Tag reagent set. , 2019, Analytical chemistry.

[16]  B. Habermann,et al.  Compromised Mitochondrial Protein Import Acts as a Signal for UPRmt. , 2019, Cell reports.

[17]  Jianyi(Jay) Zhang,et al.  Precisely Control Mitochondria with Light to Manipulate Cell Fate Decision. , 2019, Biophysical journal.

[18]  Premal Shah,et al.  A tRNA modification balances carbon and nitrogen metabolism by regulating phosphate homeostasis , 2019, eLife.

[19]  Susan E. Abbatiello,et al.  Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry. , 2019, Analytical chemistry.

[20]  Christopher S. Hughes,et al.  Single-pot, solid-phase-enhanced sample preparation for proteomics experiments , 2018, Nature Protocols.

[21]  Katie J. Clowers,et al.  ACP Acylation Is an Acetyl-CoA-Dependent Modification Required for Electron Transport Chain Assembly. , 2018, Molecular cell.

[22]  M. Haigis,et al.  The multifaceted contributions of mitochondria to cellular metabolism , 2018, Nature Cell Biology.

[23]  C. Hill,et al.  Vms1p is a release factor for the ribosome-associated quality control complex , 2018, Nature Communications.

[24]  Jia Gu,et al.  fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.

[25]  M. Karas,et al.  Acyl modification and binding of mitochondrial ACP to multiprotein complexes. , 2017, Biochimica et biophysica acta. Molecular cell research.

[26]  M. Cárdenas,et al.  Phosphate is the third nutrient monitored by TOR in Candida albicans and provides a target for fungal-specific indirect TOR inhibition , 2017, Proceedings of the National Academy of Sciences.

[27]  Andrew J. F. Valente,et al.  A simple ImageJ macro tool for analyzing mitochondrial network morphology in mammalian cell culture. , 2017, Acta histochemica.

[28]  Holger Klein,et al.  dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data , 2016, BMC Bioinformatics.

[29]  F. Drepper,et al.  The Hsp70 homolog Ssb and the 14-3-3 protein Bmh1 jointly regulate transcription of glucose repressed genes in Saccharomyces cerevisiae , 2016, Nucleic acids research.

[30]  R. Deberardinis,et al.  TCA Cycle and Mitochondrial Membrane Potential Are Necessary for Diverse Biological Functions. , 2016, Molecular cell.

[31]  Travis E. Oliphant,et al.  Guide to NumPy , 2015 .

[32]  N. Chandel Evolution of Mitochondria as Signaling Organelles. , 2015, Cell metabolism.

[33]  Mathias Wilhelm,et al.  A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets , 2015, Molecular & Cellular Proteomics.

[34]  G. Boucher,et al.  Mitochondrial Vulnerability and Increased Susceptibility to Nutrient-Induced Cytotoxicity in Fibroblasts from Leigh Syndrome French Canadian Patients , 2015, PloS one.

[35]  M. Helm,et al.  Phosphorylation of Elp1 by Hrr25 Is Required for Elongator-Dependent tRNA Modification in Yeast , 2015, PLoS genetics.

[36]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[37]  Jeroen Krijgsveld,et al.  Ultrasensitive proteome analysis using paramagnetic bead technology , 2014, Molecular systems biology.

[38]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[39]  M. Minczuk,et al.  Amino Acid Starvation Has Opposite Effects on Mitochondrial and Cytosolic Protein Synthesis , 2014, PloS one.

[40]  N. Lack,et al.  Deletion of conserved protein phosphatases reverses defects associated with mitochondrial DNA damage in Saccharomyces cerevisiae , 2014, Proceedings of the National Academy of Sciences.

[41]  J. Rutter,et al.  Hallmarks of a new era in mitochondrial biochemistry , 2013, Genes & development.

[42]  Gilles Louppe,et al.  Independent consultant , 2013 .

[43]  B. Berger,et al.  Genetic Determinants of Phosphate Response in Drosophila , 2013, PloS one.

[44]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[45]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[46]  S. Przedborski,et al.  Pink1 Kinase and Its Membrane Potential (Δψ)-dependent Cleavage Product Both Localize to Outer Mitochondrial Membrane by Unique Targeting Mode* , 2012, The Journal of Biological Chemistry.

[47]  S. Jazwinski,et al.  Loss of Mitochondrial Membrane Potential Triggers the Retrograde Response Extending Yeast Replicative Lifespan , 2012, Front. Gene..

[48]  D. Winge,et al.  The LYR Protein Mzm1 Functions in the Insertion of the Rieske Fe/S Protein in Yeast Mitochondria , 2011, Molecular and Cellular Biology.

[49]  G. Shadel,et al.  Regulation of yeast chronological life span by TORC1 via adaptive mitochondrial ROS signaling. , 2011, Cell metabolism.

[50]  Hiroyuki Noji,et al.  Rotation and structure of FoF1-ATP synthase. , 2011, Journal of biochemistry.

[51]  Gaël Varoquaux,et al.  The NumPy Array: A Structure for Efficient Numerical Computation , 2011, Computing in Science & Engineering.

[52]  Edward L. Huttlin,et al.  A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression , 2010, Cell.

[53]  R. Kölling,et al.  Cytosolic Localization of Acetohydroxyacid Synthase Ilv2 and Its Impact on Diacetyl Formation during Beer Fermentation , 2010, Applied and Environmental Microbiology.

[54]  R. Youle,et al.  Mitochondrial membrane potential regulates PINK1 import and proteolytic destabilization by PARL , 2010, The Journal of cell biology.

[55]  Wes McKinney,et al.  Data Structures for Statistical Computing in Python , 2010, SciPy.

[56]  Badrinath Roysam,et al.  A hyperfused mitochondrial state achieved at G1–S regulates cyclin E buildup and entry into S phase , 2009, Proceedings of the National Academy of Sciences.

[57]  D. Gottschling,et al.  Mitochondrial Dysfunction Leads to Nuclear Genome Instability via an Iron-Sulfur Cluster Defect , 2009, Cell.

[58]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[59]  C. Epstein,et al.  SIT4 regulation of Mig1p‐mediated catabolite repression in Saccharomyces cerevisiae , 2007, FEBS letters.

[60]  John D. Hunter,et al.  Matplotlib: A 2D Graphics Environment , 2007, Computing in Science & Engineering.

[61]  Steven P Gygi,et al.  Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry , 2007, Nature Methods.

[62]  Steven P Gygi,et al.  A probability-based approach for high-throughput protein phosphorylation analysis and site localization , 2006, Nature Biotechnology.

[63]  J. Ramírez,et al.  Deviation of carbohydrate metabolism by the SIT4 phosphatase in Saccharomyces cerevisiae. , 2006, Biochimica et biophysica acta.

[64]  K. Rosenblatt,et al.  Regulation of Fibroblast Growth Factor-23 Signaling by Klotho* , 2006, Journal of Biological Chemistry.

[65]  B. Persson,et al.  New aspects on phosphate sensing and signalling in Saccharomyces cerevisiae. , 2006, FEMS yeast research.

[66]  H. Sabbah,et al.  Inhibition of Mitochondrial Permeability Transition Pores by Cyclosporine A Improves Cytochrome c Oxidase Function and Increases Rate of ATP Synthesis in Failing Cardiomyocytes , 2005, Heart Failure Reviews.

[67]  L. Augenlicht,et al.  The intrinsic mitochondrial membrane potential of colonic carcinoma cells is linked to the probability of tumor progression. , 2005, Cancer research.

[68]  Animesh Nandi,et al.  Suppression of Aging in Mice by the Hormone Klotho , 2005, Science.

[69]  M. Cárdenas,et al.  TOR Controls Transcriptional and Translational Programs via Sap-Sit4 Protein Phosphatase Signaling Effectors , 2004, Molecular and Cellular Biology.

[70]  Hsueh‐Meei Huang,et al.  Mitochondrial Heterogeneity Within and Between Different Cell Types , 2004, Neurochemical Research.

[71]  M. A. de la Torre-Ruiz,et al.  Regulation of the Cell Integrity Pathway by Rapamycin-sensitive TOR Function in Budding Yeast* , 2002, The Journal of Biological Chemistry.

[72]  Ronald W. Davis,et al.  Functional profiling of the Saccharomyces cerevisiae genome , 2002, Nature.

[73]  W. Tatton,et al.  Mitochondrial Membrane Potential in Aging Cells , 2001, Neurosignals.

[74]  Varshal K. Davé,et al.  Genome-wide responses to mitochondrial dysfunction. , 2001, Molecular biology of the cell.

[75]  B. Böttcher ATP synthase , 2000, EMBO reports.

[76]  Xin Jie Chen,et al.  The petite mutation in yeasts: 50 years on. , 2000, International review of cytology.

[77]  Ronald W. Davis,et al.  Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. , 1999, Science.

[78]  G. Shadel,et al.  Stability of the mitochondrial genome requires an amino-terminal domain of yeast mitochondrial RNA polymerase. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[79]  M. Murphy,et al.  Quantitation and origin of the mitochondrial membrane potential in human cells lacking mitochondrial DNA. , 1999, European journal of biochemistry.

[80]  E. Garí,et al.  The Yeast Ser/Thr Phosphatases Sit4 and Ppz1 Play Opposite Roles in Regulation of the Cell Cycle , 1999, Molecular and Cellular Biology.

[81]  C. Godinot,et al.  Functional F1-ATPase essential in maintaining growth and membrane potential of human mitochondrial DNA-depleted rho degrees cells. , 1998, The Journal of biological chemistry.

[82]  Y. Oshima The phosphatase system in Saccharomyces cerevisiae. , 1997, Genes & genetic systems.

[83]  B. Brors,et al.  Two genes of the putative mitochondrial fatty acid synthase in the genome of Saccharomyces cerevisiae , 1997, Current Genetics.

[84]  Tadashi Kaname,et al.  Mutation of the mouse klotho gene leads to a syndrome resembling ageing , 1997, Nature.

[85]  H. Hatanaka,et al.  Changes in mitochondrial membrane potential during oxidative stress‐induced apoptosis in PC12 cells , 1997, Journal of neuroscience research.

[86]  V. Skulachev,et al.  High protonic potential actuates a mechanism of production of reactive oxygen species in mitochondria , 1997, FEBS letters.

[87]  N. Ogawa,et al.  The transcriptional activators of the PHO regulon, Pho4p and Pho2p, interact directly with each other and with components of the basal transcription machinery in Saccharomyces cerevisiae. , 1997, Journal of biochemistry.

[88]  S. Brody,et al.  Mitochondrial acyl carrier protein is involved in lipoic acid synthesis in Saccharomyces cerevisiae , 1997, FEBS letters.

[89]  B. Ames,et al.  Mitochondrial decay in hepatocytes from old rats: membrane potential declines, heterogeneity and oxidants increase. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[90]  J. O'connor,et al.  Aging of the liver: Age‐associated mitochondrial damage in intact hepatocytes , 1996, Hepatology.

[91]  M. Murphy,et al.  Altered mitochondrial function in fibroblasts containing MELAS or MERRF mitochondrial DNA mutations. , 1996, The Biochemical journal.

[92]  E. O’Shea,et al.  Phosphorylation of the transcription factor PHO4 by a cyclin-CDK complex, PHO80-PHO85. , 1994, Science.

[93]  K. Arndt,et al.  SIT4 protein phosphatase is required for the normal accumulation of SWI4, CLN1, CLN2, and HCS26 RNAs during late G1. , 1992, Genes & development.

[94]  M. Ratinaud,et al.  A new method for testing cell ageing using two mitochondria specific fluorescent probes , 1990, Mechanisms of Ageing and Development.

[95]  I. Lehman,et al.  Yeast RPO41 gene product is required for transcription and maintenance of the mitochondrial genome. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[96]  J. Mazat,et al.  The role of adenine nucleotide translocation in the energization of the inner membrane of mitochondria isolated from ϱ+ and ϱo strains of saccharomyces cerevisiae , 1985 .

[97]  T. Lampidis,et al.  Mitochondrial and plasma membrane potentials cause unusual accumulation and retention of rhodamine 123 by human breast adenocarcinoma-derived MCF-7 cells. , 1985, The Journal of biological chemistry.

[98]  I. Summerhayes,et al.  Unusual retention of rhodamine 123 by mitochondria in muscle and carcinoma cells. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[99]  G. Lauquin,et al.  Interaction of (3H) bongkrekic acid with the mitochondrial adenine nucleotide translocator. , 1976, Biochemistry.

[100]  L. Kováč,et al.  Oxidative phosphorylatiion in yeast. IV. Combination of a nuclear mutation affecting oxidative phosphorylation with cytoplasmic mutation to respiratory deficiency. , 1968, Biochimica et biophysica acta.